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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Interaction pattern similarity measured by Grim
You can zoom onto the graph by using the mouse to make a selection

Binding Modes are compared using Grim.
For more information, please see the following publication: Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65


Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
3oii SAH Ribosomal RNA small subunit methyltransferase NEP1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3oii SAHRibosomal RNA small subunit methyltransferase NEP1 / 1.028
3oij SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.806
3bbd SAHRibosomal RNA small subunit methyltransferase Nep1 2.1.1 0.763
4fak SAMRibosomal RNA large subunit methyltransferase H / 0.759
2qmm SAMtRNA (pseudouridine(54)-N(1))-methyltransferase / 0.756
2cx8 SAHRibosomal RNA small subunit methyltransferase E / 0.753
2egv SAMRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.743
2egw SAHRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.739
4pzk SAHPutative tRNA (cytidine(34)-2'-O)-methyltransferase / 0.730
4x3l MTARNA 2'-O ribose methyltransferase / 0.713
4cnf MTASpoU rRNA methylase / 0.698
2el3 SAHDiphthine synthase / 0.697
3o7b SAHRibosomal RNA small subunit methyltransferase Nep1 / 0.697
4kgn SAHtRNA (cytidine(34)-2'-O)-methyltransferase / 0.696
2z0y SAMRibosomal RNA small subunit methyltransferase E / 0.693
4jwf SAHtRNA (guanine(9)-N1)-methyltransferase / 0.692
4cng SAHSpoU rRNA methylase / 0.690
3vpb ADPGlutamate--LysW ligase ArgX 6.3.2 0.686
3rk1 ATPN-type ATP pyrophosphatase superfamily / 0.684
4xbo SAHtRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ 2.1.1.200 0.682
1mjh ATPUniversal stress protein MJ0577 / 0.680
1kp2 ATPArgininosuccinate synthase 6.3.4.5 0.679
2dek SAHDiphthine synthase / 0.678
2eh5 SAHDiphthine synthase / 0.678
2aj4 ANPGalactokinase 2.7.1.6 0.677
3s3t ATPUniversal stress protein / 0.676
4c5b ADPD-alanine--D-alanine ligase B 6.3.2.4 0.676
3hgm ATPTRAP-T-associated universal stress protein TeaD / 0.675
4xfj ANPArgininosuccinate synthase / 0.673
2ioa ADPBifunctional glutathionylspermidine synthetase/amidase / 0.671
4dg3 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.670
1s16 ANPDNA topoisomerase 4 subunit B / 0.669
2z08 ATPUniversal stress protein family / 0.669
2p0a ANPSynapsin-3 / 0.668
3n4k SAHtRNA (cytidine(34)-2'-O)-methyltransferase / 0.668
4uak ADPSerine/threonine-protein kinase MRCK beta 2.7.11.1 0.668
1kh3 ANPArgininosuccinate synthase / 0.667
3bbh SFGRibosomal RNA small subunit methyltransferase Nep1 2.1.1 0.667
3gyq SAM23S rRNA (adenosine(1067)-2'-O)-methyltransferase / 0.667
4dh7 ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.667
5a7y SAHtRNA (adenine(9)-N1)-methyltransferase 2.1.1.218 0.667
4i0a CMPcAMP-activated global transcriptional regulator CRP / 0.666
5c1p ADPD-alanine--D-alanine ligase / 0.666
1rfu ADPPyridoxal kinase 2.7.1.35 0.665
3nk7 SAM23S rRNA (adenosine(1067)-2'-O)-methyltransferase / 0.665
4s1h ADPPyridoxal kinase, putative / 0.665
2ha8 SAHProbable methyltransferase TARBP1 / 0.663
1cgp CMPcAMP-activated global transcriptional regulator CRP / 0.662
3fce ATPD-alanine--poly(phosphoribitol) ligase subunit 1 / 0.662
4hzf CMPcAMP-activated global transcriptional regulator CRP / 0.662
4fu0 ADPD-alanine--D-alanine ligase / 0.661
1j1z ATPArgininosuccinate synthase / 0.660
4h3y SAHtRNA (guanine-N(1)-)-methyltransferase / 0.660
1i6x CMPcAMP-activated global transcriptional regulator CRP / 0.659
2owu SAHDiphthine synthase / 0.659
2pml ANPUncharacterized protein / 0.658
3rou CMPcAMP-activated global transcriptional regulator CRP / 0.658
4bgb ADPPredicted molecular chaperone distantly related to HSP70-fold metalloproteases / 0.658
4i02 CMPcAMP-activated global transcriptional regulator CRP / 0.658
2qbu SAHPrecorrin-2 methyltransferase / 0.657
2cci ATPCyclin-dependent kinase 2 2.7.11.22 0.656
4i0b CMPcAMP-activated global transcriptional regulator CRP / 0.656
4jlp ADPAdenylate kinase / 0.656
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.656
5ce3 ADPProtein kinase YopO / 0.655
2owv SAHDiphthine synthase / 0.654
2owg SAHDiphthine synthase / 0.653
2p6l SAHDiphthine synthase / 0.653
3tw6 ADPPyruvate carboxylase / 0.653
4xw5 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.653
1cdk ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.652
2d1s SLULuciferin 4-monooxygenase 1.13.12.7 0.652
4crs AGSSerine/threonine-protein kinase N2 2.7.11.13 0.652
4f99 ADPCell division cycle 7-related protein kinase 2.7.11.1 0.651
4fmq ANPMitogen-activated protein kinase 1 2.7.11.24 0.651
4i01 CMPcAMP-activated global transcriptional regulator CRP / 0.651
2emu SAHDiphthine synthase / 0.650
4eoo ATPCyclin-dependent kinase 2 2.7.11.22 0.650